{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T22:22:24Z","timestamp":1791584544923,"version":"4.3.4"},"reference-count":37,"publisher":"Microbiology Society","issue":"6","license":[{"start":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T00:00:00Z","timestamp":1782259200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100002322","name":"Schlumberger Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100002322","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000691","name":"Academy of Medical Sciences","doi-asserted-by":"crossref","award":["SBF006\\1090"],"award-info":[{"award-number":["SBF006\\1090"]}],"id":[{"id":"10.13039\/501100000691","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,24]]},"abstract":"<jats:p>\n                    Whole-genome sequencing (WGS) of\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    (Mtb) is widely used in epidemiological investigations of recent transmission events, resulting in high-resolution strain typing. Accurate and rapid strain typing is essential for informing outbreak investigations and guiding tuberculosis control strategies. However, the gold-standard reference-guided SNP-calling pipeline currently used for strain typing relies on computationally intensive reference-mapping approaches, making it challenging to perform in many high-burden, resource-limited settings, where simplified and scalable genomic tools are urgently needed. To address these limitations, we explored reference-free methods for medium-resolution epidemiology, namely, Mtb strain (lineage) typing, using a dataset of 535 complete genomes spanning the human- and animal-adapted lineages. Illumina paired-end reads were simulated from each complete genome, assembled and analysed using three reference-free,\n                    <jats:italic>k<\/jats:italic>\n                    -mer-based tools: MASH, PopPUNK and SKA2 (split\n                    <jats:italic>k<\/jats:italic>\n                    -mer analysis). Genetic distances were generated for each method and compared with a ground truth lineage assignment from TB-Profiler. Our results demonstrated that reference-free methods can effectively distinguish Mtb lineages, with SKA2 showing the most promising performance across all datasets. SKA2 consistently recovered lineage and sub-lineage structure with high accuracy, demonstrating strong potential as an alternative to traditional WGS workflows. These findings highlight the utility of reference-free methods, particularly SKA2, for enabling accessible, scalable and rapid Mtb strain typing, while supporting genomic epidemiology with low computational resources.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001759","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T10:15:24Z","timestamp":1782296124000},"source":"Crossref","is-referenced-by-count":3,"title":["Reference-free clustering as an epidemiological tool for Mycobacterium tuberculosis lineage typing"],"prefix":"10.1099","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-6443-9098","authenticated-orcid":false,"given":"Aureliana F. C.","family":"Chilengue","sequence":"first","affiliation":[{"name":"Department of Physiological Sciences, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique"},{"name":"Department of Biosciences, Nottingham Trent University, Nottingham, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3972-5100","authenticated-orcid":false,"given":"Daniel J.","family":"Whiley","sequence":"additional","affiliation":[{"name":"Medical Technologies Innovation Facility, Nottingham Trent University, Nottingham, UK"},{"name":"Department of Biosciences, Nottingham Trent University, Nottingham, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3016-4412","authenticated-orcid":false,"given":"Kate","family":"Cox","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich, UK"},{"name":"Department of Biosciences, Nottingham Trent University, Nottingham, UK"},{"name":"University of East Anglia, Norwich, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3339-8671","authenticated-orcid":false,"given":"Maria Rosa","family":"Domingo-Sananes","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Nottingham Trent University, Nottingham, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0724-8343","authenticated-orcid":false,"given":"Conor J.","family":"Meehan","sequence":"additional","affiliation":[{"name":"Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium"},{"name":"Department of Biosciences, Nottingham Trent University, Nottingham, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.97870"},{"key":"R2","volume-title":"Global Tuberculosis Report 2023","year":"2023"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-025-01159-w"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2017.11.021"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0214-5"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms5812"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0039855"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-020-00817-3"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanmic.2025.101210"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0214088"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaa246"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkac070"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.3201\/eid2503.180894"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1101\/gr.241455.118"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1319-7"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0997-x"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1101\/gr.279449.124"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1755-7"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab199"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-019-0650-x"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty630"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1540-z"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.5895"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty633"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab301"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000217"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(12)70277-3"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0081760"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuaf017"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.3201\/eid2603.191145"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-022-07307-4"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3704"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02112-1"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-05524-0"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2018.8"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001759?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T11:16:19Z","timestamp":1782386179000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001759"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,24]]},"references-count":37,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6,24]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001759","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,24]]}}}